When Dr. Smith pulls out the Robot's battery its left arm hangs down as it normally does when it suddenly loses power (the right one stays inside its body). When John and Don reappear both arms are out and hanging down instead of just one.
When Dr. Smith pulls out the Robot's battery pack he throws it away so that it's heard rattling several feet away them. When John and Don reappear later, Don bends down at the base of the Robot to pick the battery pack up when it should have been some distance away.
In the scene in which Dr. Smith and the Robot have joined the others in the foggy purgatory, Maureen (June Lockhart) begins to laugh and has to turn her face away from the camera as Dr. Smith (Jonathan Harris) calls the Robot a "bumbling bucket of bolts."
A third deck is seen at the end of this episode. Exterior shots of the Jupiter 2 make even a second deck unfeasible, let alone an even lower deck.
When the id monster/space creature (in the form of Dr. Smith) is chasing Will down to the lower level of the ship, as he's exiting the glide tube (elevator) the gate begins to open before he presses the button.
John Robinson asks Will about the last time he saw Maureen Robinson. Will was in his cabin, and Penny and Judy were with Maureen in the galley. Will couldn't have seen his mother there since he wasn't in the same room.